xxxxaa <- read.csv("C:\\Users\\MAHE\\Downloads\\pml-training.csv", stringsAsFactors = F,na.strings = c("","NA","#DIV/0!"))
yyyybb <- read.csv("C:\\Users\\MAHE\\Downloads\\pml-testing.csv", stringsAsFactors = F,na.strings = c("","NA","#DIV/0!"))
dim(xxxxaa); dim(yyyybb)
## [1] 19622   160
## [1]  20 160
#for reproducability
set.seed(101)
zzzzcc <- createDataPartition(xxxxaa$classe, p = 0.8, list = F)
pqrs <- xxxxaa[-zzzzcc,]
xxxxaa <- xxxxaa[zzzzcc,]
dim(xxxxaa); dim(pqrs)
## [1] 15699   160
## [1] 3923  160
table(xxxxaa$classe)/nrow(xxxxaa)
## 
##         A         B         C         D         E 
## 0.2843493 0.1935155 0.1744060 0.1638958 0.1838334
dddrr <- sapply(select(xxxxaa,names(xxxxaa)[grepl("_belt",names(xxxxaa))]),
                    function(x) sum(is.na(x)))
dddrr
##            roll_belt           pitch_belt             yaw_belt 
##                    0                    0                    0 
##     total_accel_belt   kurtosis_roll_belt  kurtosis_picth_belt 
##                    0                15396                15413 
##    kurtosis_yaw_belt   skewness_roll_belt skewness_roll_belt.1 
##                15699                15395                15413 
##    skewness_yaw_belt        max_roll_belt       max_picth_belt 
##                15699                15388                15388 
##         max_yaw_belt        min_roll_belt       min_pitch_belt 
##                15396                15388                15388 
##         min_yaw_belt  amplitude_roll_belt amplitude_pitch_belt 
##                15396                15388                15388 
##   amplitude_yaw_belt var_total_accel_belt        avg_roll_belt 
##                15396                15388                15388 
##     stddev_roll_belt        var_roll_belt       avg_pitch_belt 
##                15388                15388                15388 
##    stddev_pitch_belt       var_pitch_belt         avg_yaw_belt 
##                15388                15388                15388 
##      stddev_yaw_belt         var_yaw_belt         gyros_belt_x 
##                15388                15388                    0 
##         gyros_belt_y         gyros_belt_z         accel_belt_x 
##                    0                    0                    0 
##         accel_belt_y         accel_belt_z        magnet_belt_x 
##                    0                    0                    0 
##        magnet_belt_y        magnet_belt_z 
##                    0                    0
wxyz <- sapply(select(xxxxaa,names(xxxxaa)[grepl("_arm",names(xxxxaa))]),
                   function(x) sum(is.na(x)))
wxyz
##            roll_arm           pitch_arm             yaw_arm     total_accel_arm 
##                   0                   0                   0                   0 
##       var_accel_arm        avg_roll_arm     stddev_roll_arm        var_roll_arm 
##               15388               15388               15388               15388 
##       avg_pitch_arm    stddev_pitch_arm       var_pitch_arm         avg_yaw_arm 
##               15388               15388               15388               15388 
##      stddev_yaw_arm         var_yaw_arm         gyros_arm_x         gyros_arm_y 
##               15388               15388                   0                   0 
##         gyros_arm_z         accel_arm_x         accel_arm_y         accel_arm_z 
##                   0                   0                   0                   0 
##        magnet_arm_x        magnet_arm_y        magnet_arm_z   kurtosis_roll_arm 
##                   0                   0                   0               15446 
##  kurtosis_picth_arm    kurtosis_yaw_arm   skewness_roll_arm  skewness_pitch_arm 
##               15448               15398               15445               15448 
##    skewness_yaw_arm        max_roll_arm       max_picth_arm         max_yaw_arm 
##               15398               15388               15388               15388 
##        min_roll_arm       min_pitch_arm         min_yaw_arm  amplitude_roll_arm 
##               15388               15388               15388               15388 
## amplitude_pitch_arm   amplitude_yaw_arm 
##               15388               15388
sffgff <- sapply(select(xxxxaa,
                              names(xxxxaa)[grepl("_forearm",names(xxxxaa))]),
                       function(x) sum(is.na(x)))
sffgff
##            roll_forearm           pitch_forearm             yaw_forearm 
##                       0                       0                       0 
##   kurtosis_roll_forearm  kurtosis_picth_forearm    kurtosis_yaw_forearm 
##                   15448                   15449                   15699 
##   skewness_roll_forearm  skewness_pitch_forearm    skewness_yaw_forearm 
##                   15447                   15449                   15699 
##        max_roll_forearm       max_picth_forearm         max_yaw_forearm 
##                   15388                   15388                   15448 
##        min_roll_forearm       min_pitch_forearm         min_yaw_forearm 
##                   15388                   15388                   15448 
##  amplitude_roll_forearm amplitude_pitch_forearm   amplitude_yaw_forearm 
##                   15388                   15388                   15448 
##     total_accel_forearm       var_accel_forearm        avg_roll_forearm 
##                       0                   15388                   15388 
##     stddev_roll_forearm        var_roll_forearm       avg_pitch_forearm 
##                   15388                   15388                   15388 
##    stddev_pitch_forearm       var_pitch_forearm         avg_yaw_forearm 
##                   15388                   15388                   15388 
##      stddev_yaw_forearm         var_yaw_forearm         gyros_forearm_x 
##                   15388                   15388                       0 
##         gyros_forearm_y         gyros_forearm_z         accel_forearm_x 
##                       0                       0                       0 
##         accel_forearm_y         accel_forearm_z        magnet_forearm_x 
##                       0                       0                       0 
##        magnet_forearm_y        magnet_forearm_z 
##                       0                       0
drnt <- sapply(select(xxxxaa,
                               names(xxxxaa)[grepl("_dumbbell",names(xxxxaa))]),
                        function(x) sum(is.na(x)))
drnt
##            roll_dumbbell           pitch_dumbbell             yaw_dumbbell 
##                        0                        0                        0 
##   kurtosis_roll_dumbbell  kurtosis_picth_dumbbell    kurtosis_yaw_dumbbell 
##                    15392                    15390                    15699 
##   skewness_roll_dumbbell  skewness_pitch_dumbbell    skewness_yaw_dumbbell 
##                    15391                    15389                    15699 
##        max_roll_dumbbell       max_picth_dumbbell         max_yaw_dumbbell 
##                    15388                    15388                    15392 
##        min_roll_dumbbell       min_pitch_dumbbell         min_yaw_dumbbell 
##                    15388                    15388                    15392 
##  amplitude_roll_dumbbell amplitude_pitch_dumbbell   amplitude_yaw_dumbbell 
##                    15388                    15388                    15392 
##     total_accel_dumbbell       var_accel_dumbbell        avg_roll_dumbbell 
##                        0                    15388                    15388 
##     stddev_roll_dumbbell        var_roll_dumbbell       avg_pitch_dumbbell 
##                    15388                    15388                    15388 
##    stddev_pitch_dumbbell       var_pitch_dumbbell         avg_yaw_dumbbell 
##                    15388                    15388                    15388 
##      stddev_yaw_dumbbell         var_yaw_dumbbell         gyros_dumbbell_x 
##                    15388                    15388                        0 
##         gyros_dumbbell_y         gyros_dumbbell_z         accel_dumbbell_x 
##                        0                        0                        0 
##         accel_dumbbell_y         accel_dumbbell_z        magnet_dumbbell_x 
##                        0                        0                        0 
##        magnet_dumbbell_y        magnet_dumbbell_z 
##                        0                        0
clmrrrn_2rerdrorpr <- c(names(dddrr[dddrr != 0]), 
                  names(wxyz[wxyz != 0]),
                  names(sffgff[sffgff != 0]),
                  names(drnt[drnt != 0]))
length(clmrrrn_2rerdrorpr)
## [1] 100
#dropping the cols
ftgh <- tbl_df(xxxxaa %>% 
                      select(-clmrrrn_2rerdrorpr,
                             -c(X,user_name, raw_timestamp_part_1, 
                                raw_timestamp_part_2, cvtd_timestamp, 
                                new_window,num_window)))
## Warning: `tbl_df()` is deprecated as of dplyr 1.0.0.
## Please use `tibble::as_tibble()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
## Note: Using an external vector in selections is ambiguous.
## i Use `all_of(clmrrrn_2rerdrorpr)` instead of `clmrrrn_2rerdrorpr` to silence this message.
## i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
## This message is displayed once per session.
ftgh$classe <- as.factor(ftgh$classe)
ftgh[,1:52] <- lapply(ftgh[,1:52],as.numeric)
dim(ftgh)
## [1] 15699    53
klrs <- cor(select(ftgh, -classe))
diag(klrs) <- 0
klrs <- which(abs(klrs)>0.8,arr.ind = T)
klrs <- unique(row.names(klrs))
corrplot(cor(select(ftgh,klrs)),
         type="upper", order="hclust",method = "number")
## Note: Using an external vector in selections is ambiguous.
## i Use `all_of(klrs)` instead of `klrs` to silence this message.
## i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
## This message is displayed once per session.

# binarizing data
#correlationfunnel website: https://business-science.github.io/correlationfunnel/
ytsghjjj <- ftgh %>% binarize(n_bins = 4, thresh_infreq = 0.01)
crorbr_arq <- ytsghjjj %>% correlate(target = classe__A) 
crorbr_arq %>% plot_correlation_funnel(interactive = T,limits = c(-0.5,0.5))
crororrr_brq <- ytsghjjj %>% correlate(target = classe__B)
crororrr_brq %>% plot_correlation_funnel(interactive = T,limits = c(-0.5,0.5))
crorterr_crq <- ytsghjjj %>% correlate(target = classe__C)
crorterr_crq %>% plot_correlation_funnel(interactive = T,limits = c(-0.5,0.5))
corrqwertew_drq <- ytsghjjj %>% correlate(target = classe__D)
corrqwertew_drq %>% plot_correlation_funnel(interactive = T,limits = c(-0.5,0.5))
corrqwedsw_erq <- ytsghjjj %>% correlate(target = classe__E)
corrqwedsw_erq %>% plot_correlation_funnel(interactive = T,limits = c(-0.5,0.5))
#subseting ftgh
cool_iearq <- c("magnet_arm_x", "pitch_forearm" , "magnet_dumbbell_y", 
           "roll_forearm", "gyros_dumbbell_y") 
cool_iebrq <- c("magnet_dumbbell_y", "magnet_dumbbell_x" , "roll_dumbbell" , 
           "magnet_belt_y" , "accel_dumbbell_x" )
cool_iecrq <- c("magnet_dumbbell_y", "roll_dumbbell" , "accel_dumbbell_y" , 
           "magnet_dumbbell_x", "magnet_dumbbell_z")
cool_iedrq <- c("pitch_forearm" , "magnet_arm_y" , "magnet_forearm_x",
           "accel_dumbbell_y", "accel_forearm_x")
cool_ieerq <- c("magnet_belt_y" , "magnet_belt_z" , "roll_belt", 
           "gyros_belt_z" , "magnet_dumbbell_y")
flsks_cols_qwef <- character()
for(c in c(cool_iearq,cool_iebrq,cool_iecrq,cool_iedrq,cool_ieerq)){
  flsks_cols_qwef <- union(flsks_cols_qwef, c)
}
ftgh2 <- ftgh %>% select(flsks_cols_qwef, classe)
## Note: Using an external vector in selections is ambiguous.
## i Use `all_of(flsks_cols_qwef)` instead of `flsks_cols_qwef` to silence this message.
## i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
## This message is displayed once per session.
data.frame("arm" = sum(grepl("_arm",flsks_cols_qwef)), 
           "forearm" = sum(grepl("_forearm",flsks_cols_qwef)),
           "belt" = sum(grepl("_belt",flsks_cols_qwef)),
           "dumbbell" = sum(grepl("_dumbbell",flsks_cols_qwef)))
##   arm forearm belt dumbbell
## 1   2       4    4        7
my_dens_qwedfv <- function(data, mapping, ...) {
  ggplot(data = data, mapping=mapping) +
    geom_density(..., alpha = 0.3)+scale_fill_brewer(palette="Set2") 
}
my_points_qwedfv <- function(data, mapping, ...) {
  ggplot(data = data, mapping=mapping) +
    geom_point(..., alpha = 0.1)+ scale_fill_brewer(palette="Set2") 
}
ggpairs(ftgh2, columns = 1:5,aes(color = classe),
        lower = list(continuous = my_points_qwedfv),diag = list(continuous = my_dens_qwedfv))

ggpairs(ftgh2, columns = 6:10,aes(color = classe),
        lower = list(continuous = my_points_qwedfv),diag = list(continuous = my_dens_qwedfv))

ggpairs(ftgh2, columns = 11:17,aes(color = classe),
        lower = list(continuous = my_points_qwedfv),diag = list(continuous = my_dens_qwedfv))

xxxxaaF <- xxxxaa %>% select(flsks_cols_qwef,classe)
pqrsF <- pqrs %>% select(flsks_cols_qwef,classe)
xxxxaaF[,1:17] <- sapply(xxxxaaF[,1:17],as.numeric)
pqrsF[,1:17] <- sapply(pqrsF[,1:17],as.numeric)
levels <- c("A", "B", "C", "D", "E")
preprop_obj <- preProcess(xxxxaaF[,-18],method = c("center","scale","BoxCox"))
xTrain <- predict(preprop_obj,select(xxxxaaF,-classe))
yTrain <- factor(xxxxaaF$classe,levels=levels)
xVal <- predict(preprop_obj,select(pqrsF,-classe))
yVal <- factor(pqrsF$classe,levels=levels)
trControl <- trainControl(method="cv", number=5)
#CFtree
modelCT <- train(x = xTrain,y = yTrain, 
                 method = "rpart", trControl = trControl)
#RF
modelRF <- train(x = xTrain,y = yTrain, 
                 method = "rf", trControl = trControl,verbose=FALSE, metric = "Accuracy")
#GBM
#taking too long
modelGBM <- train(x = xTrain,y = yTrain, 
                  method = "gbm",trControl=trControl, verbose=FALSE)
#SVM
modelSVM <- svm(x = xTrain,y = yTrain,
                kernel = "polynomial", cost = 10)
confusionMatrix(predict(modelCT,xVal),yVal)
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction    A    B    C    D    E
##          A 1003  330  319  294  106
##          B   19  256   20  109  103
##          C   93  173  345  240  212
##          D    0    0    0    0    0
##          E    1    0    0    0  300
## 
## Overall Statistics
##                                           
##                Accuracy : 0.4853          
##                  95% CI : (0.4696, 0.5011)
##     No Information Rate : 0.2845          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.3271          
##                                           
##  Mcnemar's Test P-Value : NA              
## 
## Statistics by Class:
## 
##                      Class: A Class: B Class: C Class: D Class: E
## Sensitivity            0.8987  0.33729  0.50439   0.0000  0.41609
## Specificity            0.6263  0.92067  0.77833   1.0000  0.99969
## Pos Pred Value         0.4888  0.50493  0.32455      NaN  0.99668
## Neg Pred Value         0.9396  0.85275  0.88147   0.8361  0.88377
## Prevalence             0.2845  0.19347  0.17436   0.1639  0.18379
## Detection Rate         0.2557  0.06526  0.08794   0.0000  0.07647
## Detection Prevalence   0.5231  0.12924  0.27097   0.0000  0.07673
## Balanced Accuracy      0.7625  0.62898  0.64136   0.5000  0.70789
confusionMatrix(predict(modelRF,xVal),yVal)
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction    A    B    C    D    E
##          A 1112    7    0    0    0
##          B    3  741    5    3    1
##          C    1    7  676   15    4
##          D    0    4    3  625    1
##          E    0    0    0    0  715
## 
## Overall Statistics
##                                           
##                Accuracy : 0.9862          
##                  95% CI : (0.9821, 0.9896)
##     No Information Rate : 0.2845          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.9826          
##                                           
##  Mcnemar's Test P-Value : NA              
## 
## Statistics by Class:
## 
##                      Class: A Class: B Class: C Class: D Class: E
## Sensitivity            0.9964   0.9763   0.9883   0.9720   0.9917
## Specificity            0.9975   0.9962   0.9917   0.9976   1.0000
## Pos Pred Value         0.9937   0.9841   0.9616   0.9874   1.0000
## Neg Pred Value         0.9986   0.9943   0.9975   0.9945   0.9981
## Prevalence             0.2845   0.1935   0.1744   0.1639   0.1838
## Detection Rate         0.2835   0.1889   0.1723   0.1593   0.1823
## Detection Prevalence   0.2852   0.1919   0.1792   0.1614   0.1823
## Balanced Accuracy      0.9970   0.9862   0.9900   0.9848   0.9958
plot(modelRF$finalModel,main="Error VS no of tree")

confusionMatrix(predict(modelGBM,xVal),yVal)
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction    A    B    C    D    E
##          A 1083   40    2    5    3
##          B   18  642   32   16   11
##          C    8   54  635   39   10
##          D    4   21   14  582    9
##          E    3    2    1    1  688
## 
## Overall Statistics
##                                           
##                Accuracy : 0.9253          
##                  95% CI : (0.9166, 0.9333)
##     No Information Rate : 0.2845          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.9055          
##                                           
##  Mcnemar's Test P-Value : 2.509e-07       
## 
## Statistics by Class:
## 
##                      Class: A Class: B Class: C Class: D Class: E
## Sensitivity            0.9704   0.8458   0.9284   0.9051   0.9542
## Specificity            0.9822   0.9757   0.9657   0.9854   0.9978
## Pos Pred Value         0.9559   0.8929   0.8512   0.9238   0.9899
## Neg Pred Value         0.9882   0.9635   0.9846   0.9815   0.9898
## Prevalence             0.2845   0.1935   0.1744   0.1639   0.1838
## Detection Rate         0.2761   0.1637   0.1619   0.1484   0.1754
## Detection Prevalence   0.2888   0.1833   0.1902   0.1606   0.1772
## Balanced Accuracy      0.9763   0.9108   0.9470   0.9452   0.9760
confusionMatrix(predict(modelSVM,xVal),yVal)
## Confusion Matrix and Statistics
## 
##           Reference
## Prediction    A    B    C    D    E
##          A 1096   40   18   17    2
##          B    1  676   15    5    6
##          C    9   40  640   45    3
##          D   10    3    9  575    9
##          E    0    0    2    1  701
## 
## Overall Statistics
##                                           
##                Accuracy : 0.9401          
##                  95% CI : (0.9322, 0.9473)
##     No Information Rate : 0.2845          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.9241          
##                                           
##  Mcnemar's Test P-Value : 1.808e-15       
## 
## Statistics by Class:
## 
##                      Class: A Class: B Class: C Class: D Class: E
## Sensitivity            0.9821   0.8906   0.9357   0.8942   0.9723
## Specificity            0.9726   0.9915   0.9701   0.9905   0.9991
## Pos Pred Value         0.9344   0.9616   0.8684   0.9488   0.9957
## Neg Pred Value         0.9927   0.9742   0.9862   0.9795   0.9938
## Prevalence             0.2845   0.1935   0.1744   0.1639   0.1838
## Detection Rate         0.2794   0.1723   0.1631   0.1466   0.1787
## Detection Prevalence   0.2990   0.1792   0.1879   0.1545   0.1795
## Balanced Accuracy      0.9773   0.9411   0.9529   0.9424   0.9857
yyyybb2 <- yyyybb %>% select(flsks_cols_qwef,problem_id)
xTest <- yyyybb2 %>% select(flsks_cols_qwef)
  
result <- data.frame("problem_id" = yyyybb$problem_id,
                     "PREDICTION_RF" = predict(modelRF,xTest),
                     "PREDICTION_GBM" = predict(modelGBM,xTest),
                     "PREDICTION_SVM" = predict(modelSVM,xTest))
result
##    problem_id PREDICTION_RF PREDICTION_GBM PREDICTION_SVM
## 1           1             E              E              C
## 2           2             A              E              A
## 3           3             A              D              B
## 4           4             E              E              C
## 5           5             E              E              A
## 6           6             E              D              C
## 7           7             E              E              B
## 8           8             B              D              A
## 9           9             A              B              E
## 10         10             E              E              E
## 11         11             A              E              C
## 12         12             A              D              C
## 13         13             E              B              E
## 14         14             A              D              B
## 15         15             E              E              B
## 16         16             E              E              A
## 17         17             E              E              C
## 18         18             B              E              A
## 19         19             E              E              A
## 20         20             E              E              E